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Went to check on hives and pull honey today. Was perplexed to see capped brood and larva above my queen excluder. I have already taken about 50 pounds of honey from this hive and supers were always pure honey. Of the 4 supers on this hive 2 of them had open and capped brood covering about 6 frames. Completely caught me off guard and wasn’t sure what to do. I probably screwed up but just took all the frames with any hint of capped or open brood and started a new hive. I have 2 medium boxes with about half the frames with honey and half with brood. I did not look real close for the queen. I probably should have shaken more bees in the new split but thought this late in the year I might be wasting my time. I am located in central MN. Any advice or help is appreciated.
 

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Shake bees in honey supers off into the brood chamber watching for queen as you go. Inspect excluder for flaws and return shaken supers above excluder. Return in three weeks and harvest.
 

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If you have an upper entrance into the supers a lost queen on a mating flight may have popped in.

Also check in lower box that the queen is still there. Seeing eggs and young brood would be good enough. I have accidentally transferred a queen up into the supers when stacking off multiple supers and inspecting lower boxes. If the queen accidentally moved above the excluder there likely would be queen cells started below.

The damaged excluder is most likely, but other crap happens!
 

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The most likely explanation is that somehow you got the queen into the box above the excluder. You could have done this during an inspection by setting the box she was in on top of another box or by moving a frame she was on, or she could have been on the queen excluder if you removed it and set it on your unstacked boxes. If you moved her and all the boxes she was laying in off to split then the home hive is now hopelessly queenless, it has no eggs or day-3 hatched brood from which to raise a queen. Inspect the home hive in four days. If you don't see queen cells in the home hive then I suggest you do a recombine, find the queen, cage her, and make sure she goes under the excluder. Release her a day later.
 

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Look in the lower boxes for brood, you may have had a supercedure and the young queen might have come into the hive above the queen excluder so it is possible to have a queen above and below which makes an easy split.
 
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